removed the "without temperature" option

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@416 60f365c0-8329-0410-b2a4-ec073aeeaa1d

src/ecopcr.c

@@ -45,8 +45,6 @@ static void PrintHelp()
         PP      "        Taxonomy id are available using the ecofind program.\n");
         PP      "        see its help typing ecofind -h for more information.\n");
         PP      "-c    : Consider that the database sequences are [c]ircular\n");
-        PP      "-t    : don't calculate tm (backward compatibility with old ecoPCR\n");
-        PP      "        output file format)\n");
         PP      "-m    : Salt correction method for Tm computation (SANTALUCIA : 1\n");
 		PP      "        or OWCZARZY:2, default=1)\n\n");
         PP      "-a    : Salt contentration in M for Tm computation (default 0.05 M)\n\n");
@@ -107,7 +105,6 @@ static void ExitUsage(stat)
 
 void printRepeat(ecoseq_t *seq,
 				 char* primer1, char* primer2,
-				 char compute_tm,
 				 PNNParams tparm,
                  PatternPtr o1, PatternPtr o2,
                  char strand, 
@@ -267,38 +264,10 @@ void printRepeat(ecoseq_t *seq,
 
 	}
 	
-	if (compute_tm)
+	tm1=nparam_CalcTwoTM(tparm,oligo1,primer1,o1->patlen) - 273.15;
-	{
+	tm2=nparam_CalcTwoTM(tparm,oligo2,primer2,o2->patlen) - 273.15;
-		tm1=nparam_CalcTwoTM(tparm,oligo1,primer1,o1->patlen) - 273.15;
+	tm = (tm1 < tm2) ? tm1:tm2;
-		tm2=nparam_CalcTwoTM(tparm,oligo2,primer2,o2->patlen) - 273.15;
+	printf("%-15s | %9d | %8d | %-20s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %c | %-32s | %2d | %5.2f | %-32s | %2d | %5.2f | %5d | %s | %s\n",
-		tm = (tm1 < tm2) ? tm1:tm2;
-		printf("%-15s | %9d | %8d | %-20s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %c | %-32s | %2d | %5.2f | %-32s | %2d | %5.2f | %5d | %s | %s\n",
-				AC,
-				seqlength,
-				taxid,
-				rank,
-				species_taxid,
-				scientificName,
-				genus_taxid,
-				genus_name,
-				family_taxid,
-				family_name,
-				superkingdom_taxid,
-				superkingdom_name,
-				strand,
-				oligo1,
-				error1,
-				tm1,
-				oligo2,
-				error2,
-				tm2,
-				amplength - o1->patlen - o2->patlen,
-				amplifia,
-				seq->DE
-			  );
-	}
-	else
-		printf("%-15s | %9d | %8d | %-20s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %8d | %-30s | %c | %-32s | %2d | %-32s | %2d | %5d | %s | %s\n",
 			AC,
 			seqlength,
 			taxid,
@@ -314,12 +283,15 @@ void printRepeat(ecoseq_t *seq,
 			strand,
 			oligo1,
 			error1,
+			tm1,
 			oligo2,
 			error2,
+			tm2,
 			amplength - o1->patlen - o2->patlen,
 			amplifia,
 			seq->DE
 		  );
+
 }
 
 int main(int argc, char **argv) 
@@ -377,7 +349,6 @@ int main(int argc, char **argv)
 	int32_t		  g=0;	
 	int32_t		  circular=0;
 	
-	char          compute_tm=1;
 	int32_t		  saltmethod=SALT_METHOD_SANTALUCIA;
 	double		  salt=0.05;
 	CNNParams     tparm;
@@ -453,22 +424,17 @@ int main(int argc, char **argv)
 		  circular = 1;
           break;
           
-								/* --------------------------- */
+
-		case 't':               /* compute tm of amplification */
-		compute_tm = 0;		    /* --------------------------- */
-		break;
 					/* --------------------------------- */
 		case 'm':               /* set salt method                   */
 					/* --------------------------------- */
 		sscanf(optarg,"%d",&(saltmethod));
-		compute_tm = 1;
 		break;
 
 					/* --------------------------------- */
 		case 'a':               /* set salt 	         */
 					/* --------------------------------- */
 		sscanf(optarg,"%lf",&(salt));
-		compute_tm = 1;
 		break;
 
 		case '?':               /* bad option           */
@@ -509,11 +475,10 @@ int main(int argc, char **argv)
 			errflag++;
 	}
 	
-	if (compute_tm)
+	nparam_InitParams(&tparm,DEF_CONC_PRIMERS,
-		nparam_InitParams(&tparm,DEF_CONC_PRIMERS,
+				 	  DEF_CONC_PRIMERS,
-				 				 DEF_CONC_PRIMERS,
+					  salt,
-								 salt,
+					  saltmethod);
-								 saltmethod);
 	                  
     if (!oligo1 || !oligo2)
     		errflag++;
@@ -534,17 +499,14 @@ int main(int argc, char **argv)
 	printf("# reverse strand oligo2 : %-32s ; oligo1c : %32s\n", o2->cpat,o1c->cpat);
 	printf("# max error count by oligonucleotide : %d\n",error_max);
 	
-	if (compute_tm)
+	double tm,tm1,tm2;
-	{
-		double tm,tm1,tm2;
 
-		tm1=nparam_CalcSelfTM(&tparm,o1->cpat,o1->patlen) - 273.15;
+	tm1=nparam_CalcSelfTM(&tparm,o1->cpat,o1->patlen) - 273.15;
-		tm2=nparam_CalcSelfTM(&tparm,o2->cpat,o2->patlen) - 273.15;
+	tm2=nparam_CalcSelfTM(&tparm,o2->cpat,o2->patlen) - 273.15;
-		tm = (tm1 < tm2) ? tm1:tm2;
+	tm = (tm1 < tm2) ? tm1:tm2;
 
-		printf("# optimal Tm for primers 1 : %5.2f\n",tm1);
+	printf("# optimal Tm for primers 1 : %5.2f\n",tm1);
-		printf("# optimal Tm for primers 2 : %5.2f\n",tm2);
+	printf("# optimal Tm for primers 2 : %5.2f\n",tm2);
-	}
 
 	printf("# database : %s\n",prefix);
 	if (lmin && lmax)
@@ -646,7 +608,7 @@ int main(int argc, char **argv)
 										if (length &&
 											(!lmin || (length >= lmin)) &&
 										    (!lmax || (length <= lmax)))
-										    printRepeat(seq,oligo1,oligo2,compute_tm,&tparm,o1,o2c,'D',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
+										    printRepeat(seq,oligo1,oligo2,&tparm,o1,o2c,'D',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
 											//printf("%s\tD\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o1Hits,o2cHits,posi,posj,scname);
 	
 									}
@@ -700,7 +662,7 @@ int main(int argc, char **argv)
 										if (length &&
 											(!lmin || (length >= lmin)) &&
 										    (!lmax || (length <= lmax)))
-										    printRepeat(seq,oligo1,oligo2,compute_tm,&tparm,o2,o1c,'R',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
+										    printRepeat(seq,oligo1,oligo2,&tparm,o2,o1c,'R',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
 											//printf("%s\tR\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o2Hits,o1cHits,posi,posj,scname);								
 									}
 								}